Variant report

Variant	rs12230104
Chromosome Location	chr12:118817830-118817831
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118812421..118814755-chr12:118815512..118818028,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111707	Chromatin interaction
ENSG00000270482	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10850968	0.84[ASN][1000 genomes]
rs11068860	1.00[EUR][1000 genomes]
rs11068864	1.00[EUR][1000 genomes]
rs11068865	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068871	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068872	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11068878	1.00[EUR][1000 genomes]
rs11068880	1.00[EUR][1000 genomes]
rs11068881	1.00[EUR][1000 genomes]
rs11068883	0.85[AMR][1000 genomes]
rs11068887	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068888	1.00[EUR][1000 genomes]
rs11068889	1.00[EUR][1000 genomes]
rs11068893	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068898	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068899	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068904	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068909	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068914	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11068915	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11068916	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068917	0.87[ASN][1000 genomes]
rs11068919	0.90[ASN][1000 genomes]
rs11068920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068922	0.92[ASN][1000 genomes]
rs11068923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068924	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068926	0.92[ASN][1000 genomes]
rs11068930	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068933	0.91[ASN][1000 genomes]
rs11068937	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11068940	1.00[EUR][1000 genomes]
rs11068941	1.00[EUR][1000 genomes]
rs11068943	1.00[EUR][1000 genomes]
rs11068945	1.00[EUR][1000 genomes]
rs12227411	1.00[EUR][1000 genomes]
rs12227974	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12228425	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12229607	0.83[ASN][1000 genomes]
rs12231358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12231845	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17586582	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17619702	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17619805	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17619932	0.86[ASN][1000 genomes]
rs2036314	0.92[ASN][1000 genomes]
rs2062520	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271007	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741444	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4442583	0.92[ASN][1000 genomes]
rs61943365	0.85[ASN][1000 genomes]
rs61943369	0.92[ASN][1000 genomes]
rs61943370	0.94[ASN][1000 genomes]
rs61943371	0.94[ASN][1000 genomes]
rs6490177	0.89[ASN][1000 genomes]
rs7132582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7296216	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888447	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118815800-118818200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:118815800-118819400	Weak transcription	Gastric	stomach
3	chr12:118815800-118824400	Weak transcription	Stomach Mucosa	stomach
4	chr12:118815800-118827400	Weak transcription	Psoas Muscle	Psoas
5	chr12:118815800-118839600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:118815800-118855200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:118816000-118819400	Weak transcription	Fetal Kidney	kidney
8	chr12:118816000-118862000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:118816200-118819600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:118816200-118819600	Weak transcription	NHEK	skin
11	chr12:118816200-118820800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:118816200-118821000	Weak transcription	HSMM	muscle
13	chr12:118816200-118823200	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:118816200-118823200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:118816200-118824000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:118816200-118824000	Weak transcription	Small Intestine	intestine
17	chr12:118816200-118863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:118816400-118835600	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:118816400-118838600	Strong transcription	Fetal Stomach	stomach
20	chr12:118816400-118855000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:118816400-118855400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:118816600-118818400	Weak transcription	Brain Germinal Matrix	brain
23	chr12:118816600-118818800	Strong transcription	Esophagus	oesophagus
24	chr12:118816600-118820600	Strong transcription	Fetal Intestine Small	intestine
25	chr12:118816800-118818800	Strong transcription	Brain Hippocampus Middle	brain
26	chr12:118816800-118820200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:118816800-118820400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:118816800-118821000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:118816800-118821200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:118816800-118828800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:118816800-118831800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:118816800-118839400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:118816800-118841600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr12:118816800-118844400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:118816800-118855000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:118816800-118855200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:118816800-118855400	Strong transcription	Primary T cells from cord blood	blood
38	chr12:118816800-118856600	Strong transcription	Placenta	Placenta
39	chr12:118817000-118819600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:118817000-118820600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:118817000-118821600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:118817000-118845600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:118817000-118846000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:118817000-118855600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:118817000-118856000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr12:118817200-118818600	Strong transcription	HUVEC	blood vessel
47	chr12:118817200-118818800	Strong transcription	Primary B cells from cord blood	blood
48	chr12:118817200-118820000	Strong transcription	Brain Substantia Nigra	brain
49	chr12:118817200-118820200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:118817200-118820200	Strong transcription	Spleen	Spleen

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